Abstract: Fossil seed distributions of submerged aquatic vegetation (SAV) from dated sediment cores in tributaries of the upper Chesapeake Bay show prehistoric changes in species composition and abundance and reflect the response of SAV species to human disturbance since European settlement. The interval of time spanned by the cores includes several centuries prior to, and three centuries following, European settlement. Species diversity is greatest in the low-salinity northern and upper tributaries, while areas of higher salinity and extensive salt marshes are characterized by low diversity or absence of SAV. Mapped distributions of seed abundances show the migration from upstream to downstream in some tributaries of the brackish species Potamogeton perfoliatus, Zannichellia palustris, and Ruppia maritima following deforestation. The largest increase in SAV, represented by the highest abundance of fossilized seeds, occurred during the 1700s after Europeans first cleared the land for farms, and the largest and most widespread decline took place in the 1960s and 1970s after most of the watershed had been at one time or another cleared and heavily fertilized for agriculture. Distributions of SAV are highly variable both temporally and spatially, reflecting the dynamic nature of estuarine habitats. Despite high environmental variability, local and regional extinctions occurred only in the most recent decades, indicating a threshold response to land use changes and nutrient loading which had begun at least two centuries earlier and intensified in the mid- to late 19th century.